Reliability of dynamic and isometric upper muscle strength testing in breast cancer survivors
Breast cancer is the most common cancer in women worldwide, and its treatment usually involves a combination of many medical procedures, including surgery, chemotherapy, radiotherapy, and hormonal therapy. One of the detrimental effects on physical function is reduced upper limb muscle strength. This study aimed to evaluate upper body strength intra-day and inter-day (test-retest) reliability using the handgrip strength test (HGS) and the bilateral isometric bench press (BIBP) and the test-retest reliability of the one repetition maximum on the bench press (BP-1RM) in breast cancer survivors (BCS). Thirty-two (52.94 ± 8.99 yrs) BCS participated in this study. The muscle strength tests were performed in two different moments, three to seven days apart. Intraclass coefficient correlation (ICC) and coefficient of variation (CV) were used to assess the reliability. Standard error of measurement (SEM), typical error of measurement (TEM), and minimally detectable change (MDC) analyses were performed. The Bland-Altman analysis was used to assess the agreement between test-retest. We found a reliability that can be described as “high” to “very high” (ICC ≥ 0.88; CV ≤ 10%) for intra-day and test-retest. SEM% and MDC% were lower than 5% and 11%, respectively, for all intra-day testing. SEM% and TEM% ranged from 3% to 11%, and MDC% ranged from 9% to 23% in the test-retest reliability. The agreement demonstrated a systematic bias ranging from 2.3% to 6.0% for all testing, and a lower systematic bias may be presented in the non-treated side assessed by HGS and BIBP. HGS, BIBP, and BP-1RM assessments are reliable for measuring upper-body muscle strength in BCS.
Santos et al. (2024) Reliability of dynamic and isometric upper muscle strength testing in breast cancer survivors. PeerJ 12:e17576 https://doi.org/10.7717/peerj.17576
Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes
Pre-harvest sprouting (PHS) is one of the important abiotic stresses in mungbean which significantly reduces yield and quality of the produce. This study was conducted to evaluate the genetic variability for tolerance to pre-harvest sprouting in diverse mungbean genotypes while simultaneously deciphering the association of yield contributing traits with PHS. Eighty-three diverse mungbean genotypes (23 released varieties, 23 advanced breeding lines and 37 exotic germplasm lines) were investigated for tolerance to PHS, water imbibition capacities by pods, pod and seed physical traits. Wide variation in PHS was recorded which ranged between 17.8% to 81% (mean value 54.34%). Germplasm lines exhibited higher tolerance to PHS than the high-yielding released varieties. Correlation analysis revealed PHS to be positively associated with water imbibition capacity by pods (r = 0.21) and germinated pod % (r = 0.78). Pod length (r = −0.13) and seeds per pod (r = −0.13) were negatively influencing PHS. Positive associations between PHS and water imbibition capacity by pods, germinated pod % and 100-seed weight was further confirmed by multivariate analysis. Small-seeded genotypes having 100-seed weight <3 g exhibited higher tolerance to PHS compared to bold-seeded genotypes having 100-seed weight more than 3.5 g. Fresh seed germination among the selected PHS tolerant and susceptible genotypes ranged from 42% (M 204) to 98% (Pusa 1131). A positive association (r = 0.79) was recorded between fresh seed germination and PHS. Genotypes M 1255, M 145, M 422, M 1421 identified as potential genetic donors against PHS could be utilized in mungbean breeding programs.
Gupta et al. (2024) Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes. PeerJ 12:e17609 https://doi.org/10.7717/peerj.17609
Comparison of selective laser melting and stereolithography etching templates for guided endodontics
Background With the increasing application of guided endodontics to treat complex root canal treatment, the entire process of root canal treatment has become more precise, reducing damage to tooth structure and improving success rates. However, due to the limitations of the operating space, the use of guided endodontic templates in posterior root canal treatment is less common. This study aims to compare the accuracy and reliability of selective laser melting (SLM) and traditional stereolithography etching (SLA) guided endodontic templates for posterior root canals, providing better treatment strategies for posterior root canal treatment. Methods The teeth were randomly assigned to either SLM or SLA group. Preoperative cone-beam computed tomography (CBCT) and a three-dimensional (3D) scanner were used to establish the 3D root canal system and the accurate occlusal models of the teeth. The virtual access to the canal access was designed using Mimics 19.0 and 3-Matic 11.0. The endodontic access was performed based on either SLM or SLA templates. The accuracy of endodontic preparation was measured in three-dimensions by calculating deviations from planned accesses. The template height and tooth substance loss rates in each group were measured. Results SLM-guided templates have a low average deviation at the entry point and apical portion of the bur of total posterior teeth (including premolars and molars) and individual molars (P < 0.05). Moreover, there was a significant difference in angular deviations and height of template in total posterior teeth and individual molars (P < 0.05). The mean substance loss rate of the SLA group was slightly greater than that of the SLM group, but the difference was not statistically (P > 0.05). Conclusions SLM-guided endodontics provides a more predictable and precise location of root canal orifice for the treatment of posterior teeth.
Zhang et al. (2024) Comparison of selective laser melting and stereolithography etching templates for guided endodontics. PeerJ 12:e17646 https://doi.org/10.7717/peerj.17646
Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues
The sweetpotato whitefly, Bemisia tabaci MEAM1, is one of the most devastating pests of row-crop vegetables worldwide, damaging crops directly through feeding and indirectly through the transmission of many different viruses, including the geminivirus Tomato yellow leaf curl virus (TYLCV). Y-tube olfactometer tests were conducted at different stages of TYLCV infection in tomatoes to understand how TYLCV affects B. tabaci behavior. We also recorded changes in tomato hosts’ color and volatile profiles using color spectrophotometry and gas chromatography-mass spectrometry (GC-MS). We found that the infection status of B. tabaci and the infection stage of TYLCV influenced host selection, with uninfected whiteflies showing a preference for TYLCV-infected hosts, especially during the late stages of infection. Viruliferous B. tabaci attraction to visual targets significantly differed from non-viruliferous B. tabaci. Late-stage infected hosts had larger surface areas reflecting yellow-green wavelengths and higher emissions of methyl salicylate in their volatile profiles. These findings shed new light on several critical mechanisms involved in the viral manipulation of an insect vector and its economically important host.
Paris et al. (2024) Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues. PeerJ 12:e17665 https://doi.org/10.7717/peerj.17665
An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh
Despite their overlooked status, weeds are increasingly recognized for their therapeutic value, aligning with historical reliance on plants for medicine and nutrition. This study investigates the medicinal potential of native weed species in Bangladesh, specifically pigments, antioxidants, and free radical scavenging abilities. Twenty different medicinal weed species were collected from the vicinity of Khulna Agricultural University and processed in the Crop Botany Department Laboratory. Pigment levels were determined using spectrophotometer analysis, and phenolics, flavonoids, and DPPH were quantified accordingly. Chlorophyll levels in leaves ranged from 216.70 ± 9.41 to 371.14 ± 28.67 µg g−1 FW, and in stems from 51.98 ± 3.21 to 315.89 ± 17.19 µg g−1 FW. Flavonoid content also varied widely, from 1,624.62 ± 102.03 to 410.00 ± 115.58 mg CE 100 g−1 FW in leaves, and from 653.08 ± 32.42 to 80.00 ± 18.86 mg CE 100 g−1 FW in stems. In case of phenolics content Euphorbia hirta L. displaying the highest total phenolic content in leaves (1,722.33 ± 417.89 mg GAE 100 g−1 FW) and Ruellia tuberosa L. in stems (977.70 ± 145.58 mg GAE 100 g−1 FW). The lowest DPPH 2.505 ± 1.028 mg mL−1was found in Heliotropium indicum L. leaves. Hierarchical clustering links species with pigment, phenolic/flavonoid content, and antioxidant activity. PCA, involving 20 species and seven traits, explained 70.07% variability, with significant PC1 (14.82%) and PC2 (55.25%). Leaves were shown to be superior, and high-performing plants such as E. hirta and H. indicum stood out for their chemical composition and antioxidant activity. Thus, this research emphasizes the value of efficient selection while concentrating on the therapeutic potential of native weed species.
Sumi et al. (2024) An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh. PeerJ 12:e17698 https://doi.org/10.7717/peerj.17698
Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes
Chromosomal fusions play an integral role in genome remodeling and karyotype evolution. Fusions that join a sex chromosome to an autosome are particularly abundant across the tree of life. However, previous models on the establishment of such fusions have not accounted for the physical structure of the chromosomes. We predict a fusion joining an autosome to the pseudoautosomal region (PAR) of a sex chromosome will not remain stable, and the fusion will switch from the X to the Y chromosome each generation due to recombination. We have produced a forward-time population genetic simulation to explore the outcomes of fusions to both the PAR and non-PAR of sex chromosomes. The model can simulate the fusion of an autosome containing a sexually antagonistic locus to either the PAR or non-PAR end of a sex chromosome. Our model is diploid, two-locus, and biallelic. Our results show a clear pattern where fusions to the non-PAR are favored in the presence of sexual antagonism, whereas fusions to the PAR are disfavored in the presence of sexual antagonism.
Wilhoit et al. (2024) Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes. PeerJ 12:e17740 https://doi.org/10.7717/peerj.17740
Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma
Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performed. Conclusion Three target genes identified by machine learning: BUB1B, CENPF, and PLK1 play key roles in LUAD development of lung adenocarcinoma.
Li et al. (2024) Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma. PeerJ 12:e17746 https://doi.org/10.7717/peerj.17746
Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus)
The “paradox of sex” refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have arisen via recent mutation after the transition to parthenogenesis. Thus, these recent SNPs are consistent with the hypothesis that purifying selection is less effective against new mutations in asexual lineages, but only over long time scales. This system provides a useful model for future studies on the evolutionary tradeoffs between sexual and asexual reproduction in nature.
Yarbrough et al. (2024) Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus). PeerJ 12:e17780 https://doi.org/10.7717/peerj.17780
Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo
Background Colletotrichum fructicola is a predominant anthracnose species in Camellia oleifera, causing various adverse effects. Traditional intercropping Vernicia fordii with C. oleifera may enhance anthracnose resistance, but the mechanism remains elusive. Methods We utilized UPLC-MS/MS and acid-base detection to identify the major antimicrobial alkaloid components in the V. fordii leaf extract. Subsequently, by adding different concentrations of V. fordii leaf extract for cultivating C. fructicola, with untreated C. fructicola as a control, we investigated the impact of the V. fordii leaf extract, cell wall integrity, cell membrane permeability, MDA, and ROS content changes. Additionally, analysis of key pathogenic genes of C. fructicola confirmed that the V. fordii leaf extract inhibits the growth of the fungus through gene regulation. Results This study discovered the alkaloid composition of V. fordii leaf extract by UPLC-MS/MS and acid-base detection, such as trigonelline, stachydrine, betaine, and O-Phosphocholine. V. fordii leaf extract successfully penetrated C. fructicola mycelia, damaged cellular integrity, and increased ROS and MDA levels by 1.75 and 2.05 times respectively, thereby inhibiting C. fructicola proliferation. By analyzing the key pathogenic genes of C. fructicola, it was demonstrated that the antifungal function of V. fordii leaf extract depends mainly on the regulation of RAB7 and HAC1 gene expression. Therefore, this study elucidates the mechanism of V. fordii -C. oleifera intercropping in strengthening anthracnose resistance in C. oleifera, contributing to efficient C. oleifera cultivation.
Ge et al. (2024) Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo. PeerJ 12:e17607 https://doi.org/10.7717/peerj.17607
Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States
Objective Surveillance is critical for the rapid implementation of control measures for diseases caused by aerially dispersed plant pathogens, but such programs can be resource-intensive, especially for epidemics caused by long-distance dispersed pathogens. The current cucurbit downy mildew platform for monitoring, predicting and communicating the risk of disease spread in the United States is expensive to maintain. In this study, we focused on identifying sites critical for surveillance and treatment in an attempt to reduce disease monitoring costs and determine where control may be applied to mitigate the risk of disease spread. Methods Static networks were constructed based on the distance between fields, while dynamic networks were constructed based on the distance between fields and wind speed and direction, using disease data collected from 2008 to 2016. Three strategies were used to identify highly connected field sites. First, the probability of pathogen transmission between nodes and the probability of node infection were modeled over a discrete weekly time step within an epidemic year. Second, nodes identified as important were selectively removed from networks and the probability of node infection was recalculated in each epidemic year. Third, the recurring patterns of node infection were analyzed across epidemic years. Results Static networks exhibited scale-free properties where the node degree followed a power-law distribution. Betweenness centrality was the most useful metric for identifying important nodes within the networks that were associated with disease transmission and prediction. Based on betweenness centrality, field sites in Maryland, North Carolina, Ohio, South Carolina and Virginia were the most central in the disease network across epidemic years. Removing field sites identified as important limited the predicted risk of disease spread based on the dynamic network model. Conclusions Combining the dynamic network model and centrality metrics facilitated the identification of highly connected fields in the southeastern United States and the mid-Atlantic region. These highly connected sites may be used to inform surveillance and strategies for controlling cucurbit downy mildew in the eastern United States.
Ojwang’ et al. (2024) Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States. PeerJ 12:e17649 https://doi.org/10.7717/peerj.17649